The abundance of sea cucumbers (Phylum Echinodermata: Class Holothuroidea) in Malaysian waters has been gradually declining in past decades. Due to the lack of recent studies on the status of sea cucumber populations in Kudat, Sabah, Malaysia, this study was conducted. This study aimed to identify the species of a timun laut morphospecies i.e. Holothuria (Metriatyla) scabra and two gamat morphospecies i.e. Stichopus horrens and Stichopus ocellatus that were collected from Limau Limawan based on ossicle shapes and non-protein-coding 12S mitochondrial rRNA gene sequences. A number of five main ossicle shapes were microscopically identified without microscopic size measurement i.e. rod, plate, rosette, button and table. However, a number of ossicle shapes for S. horrens and S. ocellatus recorded in the previous studies were not observed in this study and this could be due to the body deformation of the specimens. Interestingly, five specimens of H. scabra exhibited additional ossicle shapes other than the smooth button and the table. Despite the absence of common ossicles and the presence of additional ossicle shapes, 12S mitochondrial rRNA gene sequences analysed using the Basic Local Alignment Search Tool programme for Nucleotide (blastn) resulted in the species identification of the specimens of morphospecies H. scabra and S. horrens as H. scabra and S. horrens; however, the specimen of morphospecies S. ocellatus was identified only up to the genus level i.e. genus Stichopus, showing the lack of 12S mitochondrial rRNA gene sequences of S. ocellatus in the GenBank until 15 September, 2016. In total, 31 partial sequences of 12S mitochondrial rRNA gene were registered with the GenBank (Accession No.: KX913672-KX913702). The findings also suggested that species identification based on 12S mitochondrial rRNA gene sequence showed better inference than the ossicle shape identification. In summary, the three morphospecies were morphologically and genetically verified as H. scabra, S. horrens and S. ocellatus. Despite the fact that more specimens and more molecular techniques are required to generate better conclusive outcomes, the current findings give better insight into the importance of morphological and molecular approaches and the present status of the timun laut species and gamat species in Kudat.